All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

Abstract

The hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important antiviral paradigm based on disrupting the timing of genome packaging. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that the compound increases spike flexibility and improves recovery of helical secondary structure in the spike tips. Regions of the capsid-incorporated dimer that undergo correlated motion correspond to established sub-domains that pivot around the central chassis. AT130 alters patterns of correlated motion and other essential dynamics. A new conformational state of the dimer is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these sub-domains. Altogether, results describe a dynamical connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire core protein dimer.

The Hepatitis B Virus Nucleocapsid—Dynamic Compartment for Infectious Virus Production and New Antiviral Target

“…Not the least, theoretical approaches such as molecular dynamics (MD) simulations can now handle an entire capsid [ 160 ]. A recent all-atom MD simulation of HBV capsids bound with a CAM compound suggested a mechanism for crosstalk between intra- and inter-dimer interfaces and thus a way how allostery can traverse through the entire Cp dimer [ 161 ] that is in line with experimental data [ 162 ]. Another finding was a population of dimers with significantly splayed intra-dimer interface; such opening of the four-helix bundle has also been seen in experimental studies, e.g., when capsids interact with spike-binding peptides [ 163 ], or by mutation of the spike tip-located D78 residue which, again, affects the rate of assembly [ 151 ].…”

“…This is also manifest by overlapping but nonidentical resistance profiles [ 200 ]. In view of the capsid as an allosteric linkage assembly with options for intrasubunit, intradimer, and interdimer conformational crosstalk [ 149 , 196 ], supported by in silico data [ 161 ], such differences in CAM action are not really surprising. For instance, the CAM-E AT-130 and the CAM-A HAP1 expanded the capsid, while another CAM-A, HAP18, slightly contracted the particle [ 201 ].…”

Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR

“…M93, another source of disparity between the experimental and computational datasets, has a longer hydrophobic sidechain that may better pack into the core of the four-helix bundle than the valine of the simulation model. As residue 93 has been measured as the vertex of the Cp149 hinge domain ( Zhao et al, 2020 ; Pérez-Segura et al, 2021 ), loss of stabilization at this position likely contributes to the heighted motion predicted by simulation along the interface of helices and . Greater compliance of the hinge could account for increased flexibility observed for the spikes, along with partial unfolding of helix in C and D chains, which is largely maintained from the PDB 2G33 initial structure.…”

“…All-atom MD simulations can provide dynamical details at fully atomic resolution, however, owing to computational expense, sampling timescales are often limited, especially for large protein oligomers or assemblies. With increasing computational power, longer all-atom MD simulations of large systems, including complete virus capsids, have become accessible, revealing insights into functional motions observable over 1 microsecond of sampling ( Perilla et al, 2015 ; Pérez-Segura et al, 2021 ). However, as simulations must extend over a time significantly longer than the longest correlation time of interest to accurately characterize protein behavior, examination of the most interesting and biologically-relevant motions that occur over multi-microsecond and millisecond timescales remains a challenge.…”

Binding of a Pocket Factor to Hepatitis B Virus Capsids Changes the Rotamer Conformation of Phenylalanine 97

“…This SS-bridge forms rapidly in capsid like particles (CLPs) [26] and separates the protruding part of the spike from the part, which is embedded in the continuous capsid shell. The protruding part is structurally highly dynamic [27,28] and adapts its conformation to binding of inhibitory peptides [10,29] or fragments of HBs [30] by splaying the spike helices apart. In contrast, the embedded part of the spike is structurally rigid and shows little response to conformational challenges at the tips of the spikes.…”